To investigate effects of ocean acidification (OA) and their energy-dependent modulation in Emiliania huxleyi, diploid cells (RCC 1216) were acclimated to present and future CO2 partial pressures (pCO2; 380 vs. 1000 µatm) under low and high light (50 vs. 300 µmol photons m-2 s-1). Microarray-based transcriptome profiling was used to screen for cellular processes that underlie the physiological responses observed earlier (Rokitta & Rost 2012). OA was shown to influence fluxes of organic metabolites within and across compartments, and their partitioning between oxidative (e.g. glycolysis) and reductive pathways (e.g. pentose phosphate pathway), which is the likely cause for increased POC production. Furthermore, altered signal-transduction (e.g. phosphatidylinositolphosphate- and sphingosine-based signals) and membrane-potentials (e.g. by altered active ion transport) seem to be a major cause of impaired calcification under OA. While OA influenced signal-transduction and ion homeostasis independent of the light level, the effects of OA on the carbon metabolism were prominently modulated by energy availability. This interdependence of carbon metabolism and light physiology likely derives from their reliance on the redox equilibria of NAD+ and NADP+, which are cellular sensors for energy state and stress level. Due to the fundamental role of the affected processes, responses to OA are likely to occur similarly in other marine protists.